Re: pH in NAMD

From: Peter Freddolino (
Date: Thu Feb 08 2007 - 10:29:44 CST

You may want to have a look around the literature for constant pH
simulations (in general); none of these methods have been implemented in
NAMD yet, although we are interested in (and working on) them. As the
discussion by several others has pointed out, changing residue
protonation states is probably the most meaningful way to represent pH
in your system, since hydroxide/hydronium are present in such small
concentrations, and even if they are present, they probably won't have
the effect you want since they can't exchange protons with the solute ;-)


Per Jr. Greisen wrote:
> Hi
> Is it possible to change the pH in system for a NAMD simulation besides
> changing the state of the acids/base amino acids residues?

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